Advanced Topics, guidance and deep inner workings of code

I'm curious as to who has experience with working with the code in modules and in-depth workings.

As part of the efforts I'm doing, I've had to deal with some odd bugs that to remedy, require 'fixes' in core code. (And I know it's not an ideal choice, however after much searching of the forums, I can't wait for fixes in version 8...) An issue with Cron was one that I first dealt with. There was a long thread of discussion on the drupal forums about Cron, drupal_goto and other troublesome code. Now, I'm actually very new to Drupal coding, especially within modules and the like. I've been learning fast, however, it would be good to know a few people to bounce off the occasional idea or get some feedback on a variety of topics.

Also any pointers as to sources to read for learning and getting up to speed would be helpful. I've poured over the Drupal site, and the net for some. I also have a book available to me "Pro Drupal Development" which looks good.

What are the 'best practices'? Anything beyond what drupal.org/coding-standards has to say?

And some newbie questions, why did Drupal feel they needed to break PHP conventions such as naming files, 'whatever.module' instead of 'whatever.php'? It took me a bit to get my editor to do the code highlighting properly with the off naming convention.

Let me hear from you.

Thanks,
David